Merge pull request 'Add Pubmed affiliations (inferred by BIP) as actionsets' (#353) from 9117_pubmed_affiliations into beta
Reviewed-on: #353
This commit is contained in:
commit
836d7ec724
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@ -12,6 +12,7 @@ import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.function.FlatMapFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.Dataset;
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@ -57,11 +58,14 @@ public class PrepareAffiliationRelations implements Serializable {
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Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("inputPath");
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log.info("inputPath {}: ", inputPath);
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final String crossrefInputPath = parser.get("crossrefInputPath");
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log.info("crossrefInputPath: {}", crossrefInputPath);
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final String pubmedInputPath = parser.get("pubmedInputPath");
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log.info("pubmedInputPath: {}", pubmedInputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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log.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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@ -70,12 +74,28 @@ public class PrepareAffiliationRelations implements Serializable {
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isSparkSessionManaged,
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spark -> {
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Constants.removeOutputDir(spark, outputPath);
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prepareAffiliationRelations(spark, inputPath, outputPath);
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List<KeyValue> collectedFromCrossref = OafMapperUtils
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.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
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JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
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spark, crossrefInputPath, collectedFromCrossref);
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List<KeyValue> collectedFromPubmed = OafMapperUtils
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.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
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JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
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spark, pubmedInputPath, collectedFromPubmed);
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crossrefRelations
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.union(pubmedRelations)
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.saveAsHadoopFile(
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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});
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}
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private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath,
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String outputPath) {
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private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
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String inputPath,
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List<KeyValue> collectedfrom) {
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// load and parse affiliation relations from HDFS
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Dataset<Row> df = spark
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@ -92,7 +112,7 @@ public class PrepareAffiliationRelations implements Serializable {
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new Column("matching.Confidence").as("confidence"));
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// prepare action sets for affiliation relations
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df
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return df
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.toJavaRDD()
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.flatMap((FlatMapFunction<Row, Relation>) row -> {
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@ -120,8 +140,6 @@ public class PrepareAffiliationRelations implements Serializable {
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qualifier,
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Double.toString(row.getAs("confidence")));
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List<KeyValue> collectedfrom = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
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// return bi-directional relations
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return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
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@ -129,9 +147,7 @@ public class PrepareAffiliationRelations implements Serializable {
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.map(p -> new AtomicAction(Relation.class, p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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new Text(OBJECT_MAPPER.writeValueAsString(aa))));
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}
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private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,
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@ -6,9 +6,15 @@
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"paramRequired": false
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},
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{
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"paramName": "ip",
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"paramLongName": "inputPath",
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"paramDescription": "the URL from where to get the programme file",
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"paramName": "cip",
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"paramLongName": "crossrefInputPath",
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"paramDescription": "the path to get the input data from Crossref",
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"paramRequired": true
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},
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{
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"paramName": "pip",
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"paramLongName": "pubmedInputPath",
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"paramDescription": "the path to get the input data from Pubmed",
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"paramRequired": true
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},
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{
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@ -31,5 +31,6 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
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# The following is needed as a property of a workflow
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oozie.wf.application.path=${oozieTopWfApplicationPath}
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inputPath=/data/bip-affiliations/data.json
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crossrefInputPath=/data/bip-affiliations/data.json
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pubmedInputPath=/data/bip-affiliations/pubmed-data.json
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outputPath=/tmp/crossref-affiliations-output-v5
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@ -2,8 +2,12 @@
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<parameters>
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<property>
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<name>inputPath</name>
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<description>the path where to find the inferred affiliation relations</description>
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<name>crossrefInputPath</name>
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<description>the path where to find the inferred affiliation relations from Crossref</description>
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</property>
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<property>
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<name>pubmedInputPath</name>
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<description>the path where to find the inferred affiliation relations from Pubmed</description>
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</property>
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<property>
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<name>outputPath</name>
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@ -83,7 +87,7 @@
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Produces the atomic action with the inferred by BIP! affiliation relations from Crossref</name>
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<name>Produces the atomic action with the inferred by BIP! affiliation relations (from Crossref and Pubmed)</name>
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<class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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@ -96,7 +100,8 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--inputPath</arg><arg>${inputPath}</arg>
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<arg>--crossrefInputPath</arg><arg>${crossrefInputPath}</arg>
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<arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
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<arg>--outputPath</arg><arg>${outputPath}</arg>
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</spark>
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<ok to="End"/>
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@ -74,17 +74,22 @@ public class PrepareAffiliationRelationsTest {
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@Test
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void testMatch() throws Exception {
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String affiliationRelationsPath = getClass()
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String crossrefAffiliationRelationPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
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.getPath();
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String pubmedAffiliationRelationsPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
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.getPath();
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String outputPath = workingDir.toString() + "/actionSet";
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PrepareAffiliationRelations
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath", affiliationRelationsPath,
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"-crossrefInputPath", crossrefAffiliationRelationPath,
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"-pubmedInputPath", pubmedAffiliationRelationsPath,
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"-outputPath", outputPath
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});
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@ -101,7 +106,7 @@ public class PrepareAffiliationRelationsTest {
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// );
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// }
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// count the number of relations
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assertEquals(20, tmp.count());
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assertEquals(40, tmp.count());
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Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
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dataset.createOrReplaceTempView("result");
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@ -112,7 +117,7 @@ public class PrepareAffiliationRelationsTest {
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// verify that we have equal number of bi-directional relations
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Assertions
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.assertEquals(
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10, execVerification
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20, execVerification
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.filter(
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"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
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.collectAsList()
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@ -120,7 +125,7 @@ public class PrepareAffiliationRelationsTest {
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Assertions
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.assertEquals(
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10, execVerification
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20, execVerification
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.filter(
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"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
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.collectAsList()
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